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SomaticSignatures

The SomaticSignatures package offers the framework for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.

https://github.com/juliangehring/somaticsignatures

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 9 committers (11.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.7%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioinformatics proteomics mass-spectrometry bioconductor visualisation spatial-proteomics proteomics-data rmarkdown regionreport
Last synced: 11 months ago · JSON representation

Repository

The SomaticSignatures package offers the framework for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.

Basic Info
Statistics
  • Stars: 22
  • Watchers: 3
  • Forks: 7
  • Open Issues: 0
  • Releases: 0
Archived
Created over 12 years ago · Last pushed about 6 years ago
Metadata Files
Readme License

README.md

SomaticSignatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

For details about usage, installation and methodology, please refer to the SomaticSignatures package page in the Bioconductor repository.

Owner

  • Name: Julian Gehring
  • Login: juliangehring
  • Kind: user
  • Company: Illumina

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 77
  • Total Committers: 9
  • Avg Commits per committer: 8.556
  • Development Distribution Score (DDS): 0.234
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Julian Gehring j****g@g****m 59
Bioconductor Git-SVN Bridge b****c@b****g 5
j.gehring j****g@b****8 4
d.tenenbaum d****m@b****8 4
m.carlson m****n@b****8 1
hpages@fhcrc.org h****s@f****g@b****8 1
Julian Gehring j****g@e****e 1
s.arora s****a@b****8 1
Julian Gehring j****g 1
Committer Domains (Top 20 + Academic)
embl.de: 1 fhcrc.org: 1 bioconductor.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 9
  • Total pull requests: 0
  • Average time to close issues: 11 days
  • Average time to close pull requests: N/A
  • Total issue authors: 8
  • Total pull request authors: 0
  • Average comments per issue: 2.11
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mortunco (2)
  • saanasum (1)
  • hongenxu (1)
  • beginner984 (1)
  • fitbio (1)
  • svkazakov (1)
  • nurmians (1)
  • WinterLi1993 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 51,526 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: SomaticSignatures

Somatic Signatures

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 51,526 Total
Rankings
Dependent repos count: 0.0%
Stargazers count: 7.8%
Forks count: 8.4%
Average: 10.8%
Downloads: 17.7%
Dependent packages count: 19.9%
Maintainers (1)
jg-bioc@gmx.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • GenomicRanges * depends
  • R >= 3.1.0 depends
  • VariantAnnotation * depends
  • Biobase * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • IRanges * imports
  • NMF * imports
  • S4Vectors * imports
  • ggbio * imports
  • ggplot2 * imports
  • methods * imports
  • pcaMethods * imports
  • proxy * imports
  • reshape2 * imports
  • BSgenome.Hsapiens.1000genomes.hs37d5 * suggests
  • SomaticCancerAlterations * suggests
  • fastICA * suggests
  • ggdendro * suggests
  • knitr * suggests
  • parallel * suggests
  • sva * suggests
  • testthat * suggests